[English] 日本語
Yorodumi
- EMDB-60018: Drosophila mojavensis gustatory receptor 43a(Gr43a) in apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60018
TitleDrosophila mojavensis gustatory receptor 43a(Gr43a) in apo state
Map data
Sample
  • Complex: Tetrameric fructose-specific receptor of Drosophila mojavensis (DmGr43a)
    • Protein or peptide: Gustatory receptor
Keywordsgustatory receptors / ion channel / fructose / PROTON TRANSPORT
Function / homology
Function and homology information


male courtship behavior / chemosensory behavior / sensory perception of taste / axon / neuronal cell body / dendrite / signal transduction / plasma membrane
Similarity search - Function
7TM chemoreceptor / 7tm Chemosensory receptor
Similarity search - Domain/homology
Biological speciesDrosophila mojavensis (fry)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsChen QF / Chen RZ / Zhang R
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071202 China
National Natural Science Foundation of China (NSFC)32371261 China
CitationJournal: Cell Discov / Year: 2024
Title: Structure basis for sugar specificity of gustatory receptors in insects.
Authors: Ruizhu Chen / Ran Zhang / Lu Li / Bozhan Wang / Zhiwei Gao / Fenglian Liu / Yan Chen / Yutao Tian / Baobin Li / Qingfeng Chen /
History
DepositionMay 3, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60018.png

Downloads & links

-
Map

FileDownload / File: emd_60018.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 220 pix.
= 205.04 Å		0.93 Å/pix.
x 220 pix.
= 205.04 Å		0.93 Å/pix.
x 220 pix.
= 205.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0721
Minimum - Maximum-0.27842027 - 0.6086467
Average (Standard dev.)0.005201199 (±0.028857348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 205.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_60018_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60018_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tetrameric fructose-specific receptor of Drosophila mojavensis (D...

EntireName: Tetrameric fructose-specific receptor of Drosophila mojavensis (DmGr43a)
Components
  • Complex: Tetrameric fructose-specific receptor of Drosophila mojavensis (DmGr43a)
    • Protein or peptide: Gustatory receptor

-
Supramolecule #1: Tetrameric fructose-specific receptor of Drosophila mojavensis (D...

SupramoleculeName: Tetrameric fructose-specific receptor of Drosophila mojavensis (DmGr43a)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila mojavensis (fry)
Molecular weightTheoretical: 47.573 KDa

-
Macromolecule #1: Gustatory receptor

MacromoleculeName: Gustatory receptor / type: protein_or_peptide / ID: 1
Details: residues 428-435 correspond to the expression tag ,and residues 436-443 correspond to flexible linker.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila mojavensis (fry)
Molecular weightTheoretical: 50.13257 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEISETNIGI FYVSKLLALA PYSAKKNSKG QLEITRSWLF SIYSVCLCLI MVFLTYRGLL FDANSNIPVR MKSATSKVVT ASDVSVVVL AIVTGVYCGM FGLRATQELN TRLDKIDSTL SPYNNVKKDR WRAYAMATVS LIVIGILLGL DVGTWVRMAQ E MNISDEDT ...String:
MEISETNIGI FYVSKLLALA PYSAKKNSKG QLEITRSWLF SIYSVCLCLI MVFLTYRGLL FDANSNIPVR MKSATSKVVT ASDVSVVVL AIVTGVYCGM FGLRATQELN TRLDKIDSTL SPYNNVKKDR WRAYAMATVS LIVIGILLGL DVGTWVRMAQ E MNISDEDT ELNVQWYIPF YSLYFILTGL HINFANTAYG LGRRYKRLNQ MLRTSYLSAD KSYGNATNLV KVSTVKSISF KP MMPMALH ASLTKLNTET LPNESATKNK SLLIRAMADN HESLGKCVRL LSRFYGIAVL FILVSCLLHL VATAYFLFLE MLN KRDNGY VWVQMLWIIF HFLRLLMVVE PCHLAAREAR KTIQIVCEIE RKVFEPILVE ETKKFWQQLL VDDAEFSASG LCRV NRTIL TSFASAIATY LVILIQFQKT NGLEGGSSGG WSHPQFEK

UniProtKB: Gustatory receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4.00 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 49.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 485547
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8zdz:
Drosophila mojavensis gustatory receptor 43a(Gr43a) in apo state

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more